select_barcodes: Select specific clonotypes using barcodes from single-cell...

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Select specific clonotypes using barcodes from single-cell metadata

Description

Subsets the input immune repertoire by barcodes. Creates a vector of barcodes to subset or a vector cluster IDs and corresponding barcodes to get a list of immune repertoires corresponding to cluster IDs. Columns with clonotype counts and proportions are changed accordingly to the filtered barcodes.

Usage

select_barcodes(.data, .barcodes, .force.list = FALSE)

Arguments

.data	The data to be processed. Can be data.frame, data.table, or a list of these objects. Every object must have columns in the immunarch compatible format. immunarch_data_format Competent users may provide advanced data representations: DBI database connections, Apache Spark DataFrame from copy_to or a list of these objects. They are supported with the same limitations as basic objects. Note: each connection must represent a separate repertoire.
.barcodes	Either a character vector with barcodes or a named character/factor vector with barcodes as names and cluster IDs a vector elements. The output of Seurat's Idents function works.
.force.list	Logical. If TRUE then always returns a list, even if the result is one data frame.

Value

An immune repertoire (if ".barcodes" is a barcode vector) or a list of immune repertoires (if ".barcodes" is named vector or an output from Seurat::Idents()). Each element is an immune repertoire with clonotype barcodes corresponding to the input barcodes. The output list names are cluster names in the ".barcode" argument (Seurat::Idents() case only).

See Also

select_clusters

Examples

## Not run: 
data(immdata)
# Create a fake single-cell data
df <- immdata$data[[1]]
df$Barcode <- "AAAAACCCCC"
df$Barcode[51:nrow(df)] <- "GGGGGCCCCC"
barcodes <- "AAAAACCCCC"
df <- select_barcodes(df, barcodes)
nrow(df)

## End(Not run)

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.